Distinct Chromosome Research Articles

A case of double aneuploidy of Down and Klinefelter syndrome in an Indian infant: a detailed case report

BackgroundA variation in the number of chromosomes can lead to chromosomal disorders. These chromosomal aberrations might be related to autosomes or sex chromosomes. The most common chromosomal aberrations that are sex-linked and autosomal are Klinefelter syndrome and Down syndrome, respectively. However, the worldwide occurrence of double chromosomal aneuploidy in a single individual is relatively exceptional event and random meiotic nondisjunction events result in double aneuploidy, which causes trisomy of two distinct chromosomes. The clinical manifestations vary depending on whether aneuploidy is dominant or an amalgam of both. Moreover, double aneuploidy including autosome and sex chromosome is not often documented. In this paper, we document a case of Down–Klinefelter double aneuploidy syndrome in an Indian infant hospitalized to the neonatal care unit.Case presentationA full-term 9-month-old male infant born to a 36-year-old female with classical clinical signs of Down syndrome like epicanthus, a depressed nasal bridge, a flat face, small ears, an open mouth, thick lower lip vermilion, a protruding tongue, and a short neck was referred for cytogenetic examination, revealing a rare karyotype of 48, XXY, + 21.ConclusionDown–Klinefelter syndrome is a rare chromosomal anomaly with unique characteristics, often displaying only Down syndrome-like traits at birth. Early diagnosis can be challenging due to the lack of noticeable symptoms until puberty. Early cytogenetic investigation can detect double aneuploidy, improving the affected person's quality of life and educating family members about potential medical and psychosocial difficulties.

Efficient gene editing with an Arg-tRNA promoter-driven CRISPR/Cas9 in the rice blast fungus Pyricularia oryzae

CRISPR/Cas9 technology has been widely adopted for genome editing in a wide range of organisms, including many fungi. Pyricularia oryzae is a filamentous fungal pathogen that causes the devastating rice blast disease. However, an efficient and cost-effective CRISPR/Cas9 system for the rice blast fungus has yet to be established. Here, we report an 84-bp arginyl (Arg)-tRNA promoter-driven CRISPR/Cas9 system, which enables efficient and cost-effective gene editing in P. oryzae. Preliminary screening of three tRNAs from the 179 predicted tRNAs in P. oryzae showed that two Arg-tRNA CRISPR/Cas9 cassettes reproducibly generated MoB56 disruption efficiently. Further, five genes located on distinct chromosomes, including two previously uncharacterized genes, were randomly picked up to test the efficiency of the Mo_tRNAArg24-gRNA-Cas9 cassette. Ppg1 is a gene essential to the pathogenicity and important for mycelial growth and conidiation of P. oryzae, which is located at chromosome 2 and exhibited a relatively low gene replacement rate (< 1/500) by the traditional gene replacement approach. By using the Mo_tRNAArg24-gRNA-Cas9 cassette, Ppg1 gene disruption rate was increased up to 75.9%. In addition, Bip2, an uncharacterized genes located close to the centromere of chromosome 4, was disrupted at 66.7%. For all the five tested genes, our Mo_tRNAArg24-gRNA-Cas9 cassette showed high gene disruption efficiency in P. oryzae, ranging from 66.7% to 100%. Importantly, it rarely induces Cas9 toxicity to P. oryzae. The Mo_tRNAArg24-gRNA-Cas9 cassette described in this study can be adopted as an alternative for functional genomics study in P. oryzae.

Unveiling STRs instability in a colorectal cancer FFPE sample: a case report.

In forensic genetics, sometimes formalin-fixed paraffin-embedded (FFPE) biopsy material taken during life is the only biological sample available for individual identification or paternity testing. In most cases, this biological tissue is characterized by the presence of tumor cells characterized by instability and loss of heterozygosity of microsatellites (MSI/LOH) compared to the DNA present in cells of normal tissue.In this case report, two FFPE samples from the same male subject were available for genetic investigation: one sample with colorectal cancer tissue and the other with normal tissue (no cancerous histopathological features). The comparison of the genetic profiles obtained from DNA extracted from the two tissues showed in the tumor tissue the presence of three genomic instability phenomena affecting FGA, CSF1P0, D21S2055 loci, located on three distinct autosomal chromosomes, and one duplication phenomenon affecting the DYS438. Therefore, due to the MSI/LOH phenomena, the genetic profile acquired from the tumor tissue was distorted and thus generated a fictitious genetic profile, not corresponding to the subject's real one (normal tissue free of tumor cells).

Y and mitochondrial chromosomes in the heterogeneous stock rat population.

Genome-wide association studies typically evaluate the autosomes and sometimes the X Chromosome, but seldom consider the Y or mitochondrial (MT) Chromosomes. We genotyped the Y and MT Chromosomes in heterogeneous stock (HS) rats (Rattus norvegicus), an outbred population created from 8 inbred strains. We identified 8 distinct Y and 4 distinct MT Chromosomes among the 8 founders. However, only 2 types of each nonrecombinant chromosome were observed in our modern HS rat population (generations 81-97). Despite the relatively large sample size, there were virtually no significant associations for behavioral, physiological, metabolome, or microbiome traits after correcting for multiple comparisons. However, both Y and MT Chromosomes were strongly associated with the expression of a few genes located on those chromosomes, which provided a positive control. Our results suggest that within modern HS rats there are no Y and MT Chromosomes differences that strongly influence behavioral or physiological traits. These results do not address other ancestral Y and MT Chromosomes that do not appear in modern HS rats, nor do they address effects that may exist in other rat populations, or in other species.

Highly parallelized laboratory evolution of wine yeasts for enhanced metabolic phenotypes

Adaptive Laboratory Evolution (ALE) of microorganisms can improve the efficiency of sustainable industrial processes important to the global economy. However, stochasticity and genetic background effects often lead to suboptimal outcomes during laboratory evolution. Here we report an ALE platform to circumvent these shortcomings through parallelized clonal evolution at an unprecedented scale. Using this platform, we evolved 104 yeast populations in parallel from many strains for eight desired wine fermentation-related traits. Expansions of both ALE replicates and lineage numbers broadened the evolutionary search spectrum leading to improved wine yeasts unencumbered by unwanted side effects. At the genomic level, evolutionary gains in metabolic characteristics often coincided with distinct chromosome amplifications and the emergence of side-effect syndromes that were characteristic of each selection niche. Several high-performing ALE strains exhibited desired wine fermentation kinetics when tested in larger liquid cultures, supporting their suitability for application. More broadly, our high-throughput ALE platform opens opportunities for rapid optimization of microbes which otherwise could take many years to accomplish.

Unveiling a potential threat to forest ecosystems: molecular diagnosis of Alliaria petiolata, a newly introduced alien plant in Korea.

Identifying stages of a species invasion in a new habitat (i.e., colonization, establishment, and landscape spread) and their primary determinants in biological invasion warrants attention, as it provides vital insights for preventing non-native species from becoming pervasive invaders. However, delineating invasion stages and their associated factors can pose significant challenges due to the ambiguous distinctions between these stages. Alliaria petiolata, one of the most noxious weeds in woodland habitats, has recently been introduced to Korea and observed in a few distant locations. Although the plant's spread has been relatively slow thus far, rapid spread is highly likely in the future, given the high invasive potential reported elsewhere. We indirectly diagnose the current status of A. petiolata invasion in Korea through the assessment of genetic diversity and phylogenetic inferences using genome-wide molecular markers and cytological data. We analyzed 86 individual samples collected from two native and six introduced populations, employing 1,172 SNPs. Our analysis estimated within- and among-population genetic diversity and included two clustering analyses. Furthermore, we investigated potential gene flow and reticulation events among the sampled populations. Our data unraveled that Korean garlic mustard exhibits a hexaploid ploidy level with two distinct chromosome numbers, 2n = 36 and 42. The extent of genetic diversity measured in Korean populations was comparable to that of native populations. Using genome-wide SNP data, we identified three distinct clusters with minor gene flow, while failing to detect indications of reticulation among Korean populations. Based on the multifaceted analyses, our study provides valuable insights into the colonization process and stressed the importance of closely monitoring A. petiolata populations in Korea.

Improved assembly of the Pungitius pungitius reference genome.

The nine-spined stickleback (Pungitius pungitius) has been increasingly used as a model system in studies of local adaptation and sex chromosome evolution but its current reference genome assembly is far from perfect, lacking distinct sex chromosomes. We generated an improved assembly of the nine-spined stickleback reference genome (98.3% BUSCO completeness) with the aid of linked-read mapping. While the new assembly (v8) was of similar size as the earlier version (v7), we were able to assign 4.4 times more contigs to the linkage groups and improve the contiguity of the genome. Moreover, the new assembly contains a ∼22.8 Mb Y-linked scaffold (LG22) consisting mainly of previously assigned X-contigs, putative Y-contigs, putative centromere contigs, and highly repetitive elements. The male individual showed an even mapping depth on LG12 (pseudo X chromosome) and LG22 (Y-linked scaffold) in the segregating sites, suggesting near-pure X and Y representation in the v8 assembly. A total of 26,803 genes were annotated, and about 33% of the assembly was found to consist of repetitive elements. The high proportion of repetitive elements in LG22 (53.10%) suggests it can be difficult to assemble the complete sequence of the species' Y chromosome. Nevertheless, the new assembly is a significant improvement over the previous version and should provide a valuable resource for genomic studies of stickleback fishes.

Exploring the intersection of epigenetics, DNA repair, and immunology from studies of ICF syndrome, an inborn error of immunity.

Immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome, a rare autosomal recessive disorder, manifests with hypoglobulinemia and chromosomal instability accompanied by DNA hypomethylation. Pathological variants in the DNMT3B, ZBTB24, CDCA7, or HELLS genes underlie its etiology. Activated lymphocytes from patients often display distinctive multiradial chromosomes fused via pericentromeric regions. Recent studies have provided deeper insights into how pathological variants in ICF-related proteins cause DNA hypomethylation and chromosome instability. However, the understanding of the molecular pathogenesis underlying immunodeficiency is still in its nascent stages. In the past half-decade, the roles of CDCA7, HELLS, and ZBTB24 in classical non-homologous end joining during double-strand DNA break repair and immunoglobulin class-switch recombination (CSR) have been unveiled. Nevertheless, given the decreased all classes of immunoglobulins in most patients, CSR deficiency alone cannot fully account for the immunodeficiency. The latest finding showing dysregulation of immunoglobulin signaling may provide a clue to understanding the immunodeficiency mechanism. While less common, a subgroup of patients exhibits T-cell abnormalities alongside B-cell anomalies, including reduced regulatory T-cells and increased effector memory T- and follicular helper T-cells. The dysregulation of immunoglobulin signaling in B-cells, the imbalance in T-cell subsets, and/or satellite RNA-mediated activation of innate immune response potentially explain autoimmune manifestations in a subset of patients. These findings emphasize the pivotal roles of ICF-related proteins in both B- and T-cell functions. ICF syndrome studies have illuminated many fundamental mechanisms. Further investigations will certainly continue to unveil additional mechanisms and their interplay.

Genetic characterization, structural analysis, and detection of positive selection in small heat shock proteins of Cypriniformes and Clupeiformes.

In the current investigation, a total of 42 full-length, non-redundant small heat shock proteins (sHsp) were detected in Cyprinus carpio, Labeo rohita, Danio rerio, Salmo salar, Oncorhynchus mykiss, and Clupea harengus. The sHsp genes were classified into three groups based on phylogenetic analysis. All the sHsps were shown to have higher aliphatic index values, which is an indication that these proteins are more thermally stable. The hydrophilic nature of sHsps was deduced from the fact that all fish species had negative GRAVY scores. In all of the representative fish species, sHsp genes were assigned to distinct chromosomes in an inconsistent and unequal manner. Segmental duplications are the main events that have contributed to the expansion of the sHsp genes in all species. We were also able to determine the selective pressure that was placed on particular codons and discovered several significant coding sites within the coding region of sHsps. Eventually, diversifying positive selection was found to be connected with evolutionary changes in sHsp proteins, which showed that gene evolution controlled the fish adaption event in response to environmental conditions. Clarification of the links between sHsps and environmental stress in fish will be achieved through rigorous genomic comparison, which will also yield substantial new insights.

A high heterozygosity genome assembly of Aedes albopictus enables the discovery of the association of PGANT3 with blood-feeding behavior

The Asian tiger mosquito, Aedes albopictus, is a global invasive species, notorious for its role in transmitting dangerous human arboviruses such as dengue and Chikungunya. Although hematophagous behavior is repulsive, it is an effective strategy for mosquitoes like Aedes albopictus to transmit viruses, posing a significant risk to human health. However, the fragmented nature of the Ae. albopictus genome assembly has been a significant challenge, hindering in-depth biological and genetic studies of this mosquito. In this research, we have harnessed a variety of technologies and implemented a novel strategy to create a significantly improved genome assembly for Ae. albopictus, designated as AealbF3. This assembly boasts a completeness rate of up to 98.1%, and the duplication rate has been minimized to 1.2%. Furthermore, the fragmented contigs or scaffolds of AealbF3 have been organized into three distinct chromosomes, an arrangement corroborated through syntenic plot analysis, which compared the genetic structure of Ae. albopictus with that of Ae. aegypti. Additionally, the study has revealed a phylogenetic relationship suggesting that the PGANT3 gene is implicated in the hematophagous behavior of Ae. albopictus. This involvement was preliminarily substantiated through RNA interference (RNAi) techniques and behavioral experiment. In summary, the AealbF3 genome assembly will facilitate new biological insights and intervention strategies for combating this formidable vector of disease. The innovative assembly process employed in this study could also serve as a valuable template for the assembly of genomes in other insects characterized by high levels of heterozygosity.

Rewiring of the phosphoproteome executes two meiotic divisions in budding yeast

The cell cycle is ordered by a controlled network of kinases and phosphatases. To generate gametes via meiosis, two distinct and sequential chromosome segregation events occur without an intervening S phase. How canonical cell cycle controls are modified for meiosis is not well understood. Here, using highly synchronous budding yeast populations, we reveal how the global proteome and phosphoproteome change during the meiotic divisions. While protein abundance changes are limited to key cell cycle regulators, dynamic phosphorylation changes are pervasive. Our data indicate that two waves of cyclin-dependent kinase (Cdc28Cdk1) and Polo (Cdc5Polo) kinase activity drive successive meiotic divisions. These two distinct phases of phosphorylation are ensured by the meiosis-specific Spo13 protein, which rewires the phosphoproteome. Spo13 binds to Cdc5Polo to promote phosphorylation in meiosis I, particularly of substrates containing a variant of the canonical Cdc5Polo motif. Overall, our findings reveal that a master regulator of meiosis directs the activity of a kinase to change the phosphorylation landscape and elicit a developmental cascade.

Whole genome based identification of BAHD acyltransferase gene involved in piperine biosynthetic pathway in black pepper

Black pepper (Piper nigrum L.), a crop of the genus Piper, is an important spice that has both economic and ecological significance. It is widely regarded as the “King of Spices” because of its pungency, attributed to the presence of piperine. BAHD acyl transferase, the crucial enzyme involved in the final step in piperine biosynthesis was the focus of our study and the aim was to identify the candidate isoform involved in biosynthesis of piperine. Reference genome-based analysis of black pepper identified six BAHD-AT isoforms and mapping of these sequences revealed that the isoforms were situated on six distinct chromosomes. By using specific primers for each of these transcripts, qPCR analysis was done in different tissues as well as berry stages to obtain detectable amplification products. Expression profiles of isoforms from chromosome 6 correlated well with piperine content compared to other five isoforms, across tissues and was therefore assumed to be involved in biosynthesis of piperine. In addition to this, we could also identify the binding sites of MYB transcription factor in the cis-regulatory regions of the isoforms. We also used in-silico docking and molecular dynamics simulation to calculate the binding free energy of the ligand and confirmed that among all the isoforms, BAHD-AT from chromosome 6 had the lowest free binding energy and highest affinity towards the ligand. Our findings are expected to aid the identification of new genes connecting enzymes involved in the biosynthetic pathway of piperine, which will have major implications for future research in metabolic engineering. Communicated by Ramaswamy H. Sarma

A bi-criterion sequence-dependent scheduling problem with order deliveries.

The manufacturing sector faces unprecedented challenges, including intense competition, a surge in product varieties, heightened customization demands, and shorter product life cycles. These challenges underscore the critical need to optimize manufacturing systems. Among the most enduring and complex challenges within this domain is production scheduling. In practical scenarios, setup time is whenever a machine transitions from processing one product to another. Job scheduling with setup times or associated costs has garnered significant attention in both manufacturing and service environments, prompting extensive research efforts. While previous studies on customer order scheduling primarily focused on orders or jobs to be processed across multiple machines, they often overlooked the crucial factor of setup time. This study addresses a sequence-dependent bi-criterion scheduling problem, incorporating order delivery considerations. The primary objective is to minimize the linear combination of the makespan and the sum of weighted completion times of each order. To tackle this intricate challenge, we propose pertinent dominance rules and a lower bound, which are integral components of a branch-and-bound methodology employed to obtain an exact solution. Additionally, we introduce a heuristic approach tailored to the problem's unique characteristics, along with three refined variants designed to yield high-quality approximate solutions. Subsequently, these three refined approaches serve as seeds to generate three distinct populations or chromosomes, each independently employed in a genetic algorithm to yield a robust approximate solution. Ultimately, we meticulously assess the efficacy of each proposed algorithm through comprehensive simulation trials.

Comparative karyotypic study of fifteen cyprinids (Cyprinidae, Cyprininae) species. An insight into the chromosomal evolution of the tribe Systomini.

The family Cyprinidae is the largest freshwater fish group with 377 genera and over 3,000 described species. However, this group of fish has very limited cytogenetics and advanced molecular cytogenetics information. Therefore, in this study the karyotypes and other chromosomal characteristics of 15 species in the tribe Systomini (Cyprininae) were examined using Ag-NOR staining along with fluorescence in situ hybridization (5S and 18S rDNA). All species share a similar karyotype (2n = 50; NF = 88-100) in both sexes and no differentiated sex chromosome was observed. Chromosomes bearing NOR sites ranged from one to four pairs among the species, mostly mapped adjacent to telomeres in the short arms of distinct pairs in all analyzed species. This difference indicates an extensive rearrangement of chromosomes including genomic differences. The use of the 5S and 18S rDNA probe confirmed the Ag-NOR sites interstitially located in the telomeric regions of distinct chromosomes, characterizing an interspecies variation of these sites. In most of its analyzed species, the signals of 18S rDNA probe corresponded to the Ag-NOR regions, except in Barbonymus altus, B. gonionotus, B. schwanenfeldii and Puntius brevis having these signals on the same as Ag-NOR regions and other sites.

B-388 Clinical Performance of Xpert BCR-ABL Ultra Assay for Isoform p210 Quantitation

Abstract Background Chronic myelogenous leukemia (CML) is one of the most common hematologic neoplasms. More than 95% of patients with CML have the distinctive Philadelphia chromosome (Ph1) that results from a translocation between the chromosomes 9 and 22, and consequently in the BCR::ABL1 fusion gene. This fusion gene produces a tyrosine kinase with deregulated activity that plays a key role in the development of CML. Monitoring BCR::ABL transcript levels in patients on tyrosine kinase inhibitor (TKI) therapy using real-time quantitative PCR is standard of care in the management of CML patients. The test utilizes a quantitative, real-time reverse transcription polymerase chain reaction (RT-qPCR) to measure BCR::ABL1 to ABL1 percent ratios on the International Scale (%IS), in t(9;22) positive CML patients during monitoring of treatment with TKIs. In this context, this study evaluated clinical performance of the Xpert® BCR-ABL Ultra assay for quantitation of BCR::ABL1 p210 transcripts. Methods The clinical performance of assay was evaluated by comparison to an RT-qPCR assay routinely used in our institution, which also detects and quantifies the mRNA transcripts for the p210 translocation types and uses the ABL gene as an endogenous control. In total, 30 fresh peripheral blood samples of CML patients with the level of BCR::ABL1 transcripts (international scale, IS) between &amp;gt;50% and undetectable were enrolled in this study. All steps of protocols were performed according to manufacturer ́s instructions. Results The comparison of two assay revealed consistente molecular response (MR) level. Linear regression analysis showed high correlation between the assays (R2 = 0.974, P &amp;lt; 0.0001) The slope of regression curve were not significantly different from the value of 1 (1.003; 95% CI, range 0.943–1.069). The evaluation of MR level was identical in 21/28 (75%) samples. Two samples were excluded from the study due to failure to control ABL1 (Ct &amp;gt; 18). The median of ABL1 copies per sample was 66 011 copies (range 20 010–236 171) for conventional RT-qPCR assay. Xpert BCR-ABL Ultra reports %IS (MR), but this test does not report ABL1 copy numbers. If the Xpert BCR-ABL Ultra test reports a positive or negative result and the ABL1 Ct value is below 18, a minimum of 32 000 ABL1 copy numbers is guaranteed in the reaction. The BCR::ABL1 negativity was concordant in 2/8 samples. Conclusion We showed that the results Xpert® BCR-ABL Ultra assay (MR) are in good correlation with the results of RT-qPCR conventional method.The Xpert® BCR-ABL Ultra assay simplifies the generation of results by integrating nucleic acid extraction, amplification, and quantification of the BCR::ABL1 p210 transcripts in peripheral blood specimens. The assay turn-around-time is approximately 3 h. This does not differentiate between b2a2 or b3a2 fusion transcripts.This assay is unable to detect BCR::ABL1 p190 or other rarer translocations.

Turnover of multiple sex chromosomes in Harttia catfish (Siluriformes, Loricariidae): a glimpse from whole chromosome painting.

The remarkable fish biodiversity encompasses also great sex chromosome variability. Harttia catfish belong to Neotropical models for karyotype and sex chromosome research. Some species possess one of the three male-heterogametic sex chromosome systems, XY, X1X2Y or XY1Y2, while other members of the genus have yet uncharacterized modes of sex determination. Particularly the XY1Y2 multiple sex chromosome system shows a relatively low incidence among vertebrates, and it has not been yet thoroughly investigated. Previous research suggested two independent X-autosome fusions in Harttia which led to the emergence of XY1Y2 sex chromosome system in three of its species. In this study, we investigated evolutionary trajectories of synteny blocks involved in this XY1Y2 system by probing six Harttia species with whole chromosome painting (WCP) probes derived from the X (HCA-X) and the chromosome 9 (HCA-9) of H. carvalhoi. We found that both painting probes hybridize to two distinct chromosome pairs in Amazonian species, whereas the HCA-9 probe paints three chromosome pairs in H. guianensis, endemic to Guyanese drainages. These findings demonstrate distinct evolutionary fates of mapped synteny blocks and thereby elevated karyotype dynamics in Harttia among the three evolutionary clades.

Cytomolecular characterization of early and late condensing chromosome regions in some Annonaceae species

Abstract The condensation patterns (CPs) of prophase chromosomes represent poorly explored and little understood karyotype features. Three distinct chromosome domains are observed in conventionally stained prophases of most angiosperms with small chromosomes: heterochromatin and early condensing euchromatin (ECEu), which are observed as early condensing regions (ECRs), and late condensing euchromatin or late condensing regions (LCRs). All three prophase domains have been often reported in the Annonaceae species. To gain a better understanding of these regions, we investigated the CPs, heterochromatic bands, and rDNA sites in seven Annona species with 2n = 14, 28, and 54 and Xylopiafrutescens with 2n = 16. Besides, histone H4K5 acetylation, telomeric sites, and DNA methylation were analysed in some of these species. LCRs corresponded to a small hyperacetylated, and hypomethylated fraction of the metaphase chromosomes. During interphase, the chromocentres displayed variable proportions of heterochromatin and ECEu. The LCRs and ECRs were conserved even between disploid and polyploid species, whereas rDNA sites and heterochromatic bands varied in number and location. Our data suggest that chromatin compartmentalization in ECR and LCR regions may represent the simplest functional organization of the small chromosomes of Annonaceae, while the remaining characters are less relevant.

Mesoscale, long-time mixing of chromosomes and its connection to polymer dynamics.

Chromosomes are arranged in distinct territories within the nucleus of animal cells. Recent experiments have shown that these territories overlap at their edges, suggesting partial mixing during interphase. Experiments that knock-down of condensin II proteins during interphase indicate increased chromosome mixing, which demonstrates control of the mixing. In this study, we use a generic polymer simulation to quantify the dynamics of chromosome mixing over time. We introduce the chromosome mixing index, which quantifies the mixing of distinct chromosomes in the nucleus. We find that the chromosome mixing index in a small confinement volume (as a model of the nucleus), increases as a power-law of the time, with the scaling exponent varying non-monotonically with self-interaction and volume fraction. By comparing the chromosome mixing index with both monomer subdiffusion due to (non-topological) intermingling of chromosomes as well as even slower reptation, we show that for relatively large volume fractions, the scaling exponent of the chromosome mixing index is related to Rouse dynamics for relatively weak chromosome attractions and to reptation for strong attractions. In addition, we extend our model to more realistically account for the situation of the Drosophila chromosome by including the heterogeneity of the polymers and their lengths to account for microphase separation of euchromatin and heterochromatin and their interactions with the nuclear lamina. We find that the interaction with the lamina further impedes chromosome mixing.

Genome-Transcriptome Transition Approaches to Characterize Anthocyanin Biosynthesis Pathway Genes in Blue, Black and Purple Wheat.

Colored wheat has gained enormous attention from the scientific community, but the information available on the anthocyanin biosynthetic genes is very minimal. The study involved their genome-wide identification, in silico characterization and differential expression analysis among purple, blue, black and white wheat lines. The recently released wheat genome mining putatively identified eight structural genes in the anthocyanin biosynthesis pathway with a total of 1194 isoforms. Genes showed distinct exon architecture, domain profile, regulatory elements, chromosome emplacement, tissue localization, phylogeny and synteny, indicative of their unique function. RNA sequencing of developing seeds from colored (black, blue and purple) and white wheats identified differential expressions in 97 isoforms. The F3H on group two chromosomes and F3'5'H on 1D chromosomes could be significant influencers in purple and blue color development, respectively. Apart from a role in anthocyanin biosynthesis, these putative structural genes also played an important role in light, drought, low temperature and other defense responses. The information can assist in targeted anthocyanin production in the wheat seed endosperm.

Karyotypic diversity: a neglected trait to explain angiosperm diversification?

Evolutionary changes in karyotype provide genetic support to organisms' differentiation and adaptation; however, the association between karyotype diversity and species diversification in flowering plants (angiosperms) remains to be fully elucidated. We sought evidence for this association within a phylogenetic framework using a dataset comprising > 413,000 worldwide chromosome counts of 66,000 angiosperms species. Karyotypic diversity (e.g., number of distinct chromosome numbers) explains species richness and diversification rates at both family and genus levels highlighting that chromosome evolution has probably played, at least, an important role in reinforcing speciation that was already initiated or completed by other geographical or ecological drivers. Thus, research programs investigating chromosome variation as a direct or indirect driver of diversification should be encouraged.